Freesurfer

freesurfer@nmr.mgh.harvard.edu

13 participants
30082 discussions

wm parcellation
by Caroline Beelen 17 May '16

17 May '16

Dear FS team, Thank you for your answers before (email: WmParc). We now realize that we've formulated our question wrong, since our problem is mainly in creating the wmparc.a2009s.mgz file. We ran the following command: mri_aparc2aseg --s <subjid> --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.a2009s.mgz --ctxseg aparc.a2009s+aseg.mgz (<subjid> was replaced by our subject and the ribbon command was set to 'noribbon' because we otherwise received the message the that the ribbon command was unknown.) If we run this command, we can extract grey matter labels with fslmaths (e.g. 11136 for the left planum temporale), but not the white matter labels we are looking for (this is 13136 for the left planum temporale). The problem seems to be in the labelling of the white matter. Many thanks. Jolijn & Caroline

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Re: [Freesurfer] ERROR: cannot unpack mosiacs without ASCII header
by Aloi, Joseph 17 May '16

17 May '16

Hi Doug, Yes, you are correct- data I have previously processed without any problems is no longer being processed. My version of freesurfer is 5.3.0; I only downloaded it a few weeks ago so I have not changed my freesurfer version recently. Thanks! Joseph Aloi Graduate Student, MD/PhD Scholars Program Department of Pharmacology and Experimental Neuroscience University of Nebraska Medical Center Neurobehavioral Research Assistant, Center For Neurobehavioral Research Boys Town National Research Hospital The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

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Big ventricles and recon-all error
by Kasper Jessen 17 May '16

17 May '16

Dear FreeSurfer group, I am having problems with a subject with very large ventricles. The recon-all exits with errors. Is it known issue that FreeSurfer is having difficulties with large ventricles? How can i solve this problem? I have read in another post, that the flag -bigventricles may solve the problem? Best regards, Kasper

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mri_coreg !
by Elijah Mak 16 May '16

16 May '16

Hi Doug and Martin, Thanks both for your responses. I am working with PK11195, AV-1451, and PiB. In general, the standard bbregister routine with init-fsl works well for AV-1451 (adjustments needed in 30% of cases) and PiB (best performance), but it completely failed with the PK data which was acquired on the same scanner. I tried running the registration using the mean image (mri_concat --mean) but it did not help too. All that being said, mri_coreg works extremely well for the PK11195 (only 3 manual adjustments needed so far for > 50 scans), so I am very grateful for this tool :) If I want to run the analyses of the various PET data in the same study, will it be of concern that I am using a mix of boundary-based (AV and PIB) and normalised mutual information (PK)? Best Wishes, Elijah Re: [Freesurfer] mri_coreg ! <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subje…> Martin Reuter <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Mon, 16 May 2016 13:23:13 -0700 <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> Hi, just wanted to mention that the --cost NMI (normalized mutual information) and MI implementations in mri_robust_register are the same as spm_coreg and now mri_coreg (if the -nosym flag is specified in robust register, else it is registering in a symmetric midspace instead into the target space). If you have cases where robust_register fails, but the other tools work, let me know, because that could indicate a bug in my code. Thanks, Martin On 05/16/2016 03:19 PM, Douglas N Greve wrote: > It is my implementation of the spm_coreg program written by John > Ashburner using normalized mutual information. I liked the spm program > so much that I put the effort into replicating its behavior in C. My > guess is that BBR was failing because the initialization was failing. > Still I like mri_coreg for PET data because the blurriness can throw BBR > off a bit. What kind of PET data do you have? > > > On 05/16/2016 03:06 PM, Elijah Mak wrote: >> Hi Doug, >> >> I just want to say that mri_coreg worked tremendously well for the >> registration of some very blurry PET-PK data. I was not getting any >> success with bbregister and init-fsl or mri_robust_register options. >> >> How does this technique differ from the boundary-based registration? >> >> Thanks a lot. >> >> Best Wishes, >> Elijah >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

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Postdoctoral position in neuroimage analysis
by Bruce Fischl 16 May '16

16 May '16

Postdoctoral Research Fellow Position Neuroimaging Analysis of Human Brain Connectivity in Dementia www.nmr.mgh.harvard.edu/working/employment#20160516 The Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging invites applications for a postdoctoral Research Fellow position at the Massachusetts General Hospital and Harvard Medical School. Funded by the BrightFocus Foundation, the project consists of human brain connectivity analysis and its application in studying Alzheimer’s disease. The appointment starts as early as September 2016, and is for two years with the possibility of a third year based on performance and the availability of funding. The project involves analyzing structural and functional brain networks through diffusion-weighted and functional MRI, and examining their relationship with different stages of dementia. In particular, we would like to identify the relative roles of direct and indirect neuronal connections. The Research Fellow will be supervised by Dr. Iman Aganj, with close collaboration with Dr. Bruce Fischl and Dr. Reisa Sperling. The candidate is required to have: · a Ph.D. in engineering, neuroscience, or a related field by the start date, · strong programming skills in MATLAB or a similar environment, and · a medical image analysis background. Familiarity and experience with any of the following will be a plus: connectomics, neuroimaging, diffusion-weighted MRI, functional MRI, graph theory, machine learning, dementia studies, mathematical modeling, Linux operating system. Interested applicants should send a cover letter describing research interests and experience, an up-to-date CV, and names and contact information of three references to: iman(a)nmr.mgh.harvard.edu

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mri_coreg !
by Elijah Mak 16 May '16

16 May '16

Hi Doug, I just want to say that mri_coreg worked tremendously well for the registration of some very blurry PET-PK data. I was not getting any success with bbregister and init-fsl or mri_robust_register options. How does this technique differ from the boundary-based registration? Thanks a lot. Best Wishes, Elijah

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Longitudinal analysis: creat cluster ROI and extract baseline and followup values
by Liu Y 16 May '16

16 May '16

Hi Freesurfers, I am using the degree of cortical atrophy between two groups. The atrophy rate had no significant difference between two groups, but the average thickness of the baseline and followup showed significant clusters in two regions between the two groups. My question is how to create the ROIs covering the clusters, and then extract the thicknesses on baseline and followup MRIs? Thanks, Yawu

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ERROR: cannot unpack mosiacs without ASCII header
by Aloi, Joseph 16 May '16

16 May '16

Hi freesurfer experts, I have recently begun to use freesurfer to do structural MRI analyses. I have been able to successfully process about 40 structural scans with recon-all thus far, but starting a few days ago, I started getting this error whenever I run recon-all: WARNING: file /Users/alojos/Applications/freesurfer/subjects/sub_9999.dcm does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header Darwin nerc130622.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan 11 18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64 recon-all -s sub_9999 exited with ERRORS at Mon May 16 08:43:24 CDT 2016 Here are a few of the troubleshooting steps I’ve tried to track down the cause of the error: - - Re-run recon-all with a couple of scans from my dataset that I have already successfully processed - - Re-run recon-all the same datasets but on a different computer - - Re-convert the scans from .ima files to dicoms in osirix, then run recon-all For all of these steps, I have gotten the exact same error message. The files should be anonymized, since I used osirix’s “anonymize and convert” function to generate the dicom files (the scans were given to me as .ima files). Any suggestions on what to try next? Thank you! Joseph Aloi The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

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Freesurfer program for 7 Tesla
by konasale prasad 16 May '16

16 May '16

Dear FSL experts, We are trying to run freesurfer volume measurements, primarily subcortical regions along with cortical surface area and thickness. We are also interested in hippocampal subfields and shape analysis. I was wondering whether the program would be reliable compared to 3T (that we have done quite a few). Are there any known problems? If there are, please let me know the work arounds. Thanks,

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reference for using T2 to improve pial surface
by Ritobrato Datta 16 May '16

16 May '16

Hi All, Can someone point to a reference which shows the advantage of using T2 alongside T1 to improve the gray - pial boundary ? Thank you, Ri

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Freesurfer